The widespread use of nanomaterials in biomedical applications has been accompanied by an increasing interest in understanding their interactions with tissues, cells, and biomolecules, and in particular, on how they might affect the integrity of cell membranes and proteins. In this mini‐review, we present a summary of some of the recent studies on this important subject, especially from the point of view of large scale molecular simulations. The carbon‐based nanomaterials and noble metal nanoparticles are the main focus, with additional discussions on quantum dots and other nanoparticles as well. The driving forces for adsorption of fullerenes, carbon nanotubes, and graphene nanosheets onto proteins or cell membranes are found to be mainly hydrophobic interactions and the so‐called π–π stacking (between aromatic rings), while for the noble metal nanoparticles the long‐range electrostatic interactions play a bigger role. More interestingly, there are also growing evidences showing that nanotoxicity can have implications in de novo design of nanomedicine. For example, the endohedral metallofullerenol Gd@C82(OH)22 is shown to inhibit tumor growth and metastasis by inhibiting enzyme MMP‐9, and graphene is illustrated to disrupt bacteria cell membranes by insertion/cutting as well as destructive extraction of lipid molecules. These recent findings have provided a better understanding of nanotoxicity at the molecular level and also suggested therapeutic potential by using the cytotoxicity of nanoparticles against cancer or bacteria cells. WIREs Syst Biol Med 2014, 6:265–279. doi: 10.1002/wsbm.1271This article is categorized under: Biological Mechanisms > Chemical Biology Analytical and Computational Methods > Computational Methods